The paper, swiftly rejected by authorities in Pyongyang, uncovered a pattern of human rights abuses, the head of the independent inquiry told the UN Human Rights Council.
There have long been concerns about reports of atrocities including executions and torture, but they have largely been overshadowed by international alarm about North Korea's nuclear weapons.
The report came after pressure by Japan, South Korea and Western powers to investigate and begin building a case for possible criminal prosecution.
Inquiry head, Michael Kirby, said the findings were based on testimony from North Korean exiles, including former political prison camp inmates, given at hearings in Seoul and Tokyo.
The former justice of Australia's top court said: "I have been a judge for a very long time and I'm pretty hardened to testimony.
"But the testimony I saw in Seoul and in Tokyo brought tears to my eyes on several occasions."
North Korean diplomat Kim Yong Ho said the inquiry was a defamatory "political plot" to force regime change.